Multiple sequence alignment - TraesCS1D01G010700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G010700 chr1D 100.000 7969 0 0 1 7969 5510403 5518371 0.000000e+00 14717.0
1 TraesCS1D01G010700 chr1D 92.857 84 4 2 3957 4039 370323729 370323647 3.910000e-23 121.0
2 TraesCS1D01G010700 chr1A 94.718 5112 195 33 856 5932 7178189 7183260 0.000000e+00 7875.0
3 TraesCS1D01G010700 chr1A 89.871 2093 133 37 5933 7969 7183449 7185518 0.000000e+00 2617.0
4 TraesCS1D01G010700 chr1A 92.142 649 32 11 856 1486 6977022 6977669 0.000000e+00 898.0
5 TraesCS1D01G010700 chr1A 93.866 538 29 2 1513 2046 6977661 6978198 0.000000e+00 808.0
6 TraesCS1D01G010700 chr1B 93.925 1926 84 16 4027 5923 8251730 8253651 0.000000e+00 2878.0
7 TraesCS1D01G010700 chr1B 89.572 2081 134 40 5933 7969 8253739 8255780 0.000000e+00 2564.0
8 TraesCS1D01G010700 chr1B 96.408 1392 33 12 2567 3956 8250354 8251730 0.000000e+00 2278.0
9 TraesCS1D01G010700 chr1B 96.108 1259 39 4 1070 2325 8249061 8250312 0.000000e+00 2045.0
10 TraesCS1D01G010700 chr1B 92.982 114 2 2 856 968 8248561 8248669 2.300000e-35 161.0
11 TraesCS1D01G010700 chr3D 94.454 595 25 2 2092 2686 555196711 555197297 0.000000e+00 909.0
12 TraesCS1D01G010700 chr3D 94.286 595 26 2 2092 2686 550608301 550607715 0.000000e+00 904.0
13 TraesCS1D01G010700 chr3D 93.445 595 31 2 2092 2686 555232210 555231624 0.000000e+00 876.0
14 TraesCS1D01G010700 chr3D 92.857 84 5 1 3947 4030 110398471 110398389 3.910000e-23 121.0
15 TraesCS1D01G010700 chr7D 94.286 595 26 2 2092 2686 443545749 443545163 0.000000e+00 904.0
16 TraesCS1D01G010700 chr7D 93.548 93 4 2 3951 4042 184573352 184573443 3.880000e-28 137.0
17 TraesCS1D01G010700 chr7D 95.890 73 2 1 3958 4030 5307665 5307736 5.050000e-22 117.0
18 TraesCS1D01G010700 chr2D 93.950 595 28 2 2092 2686 385100535 385101121 0.000000e+00 893.0
19 TraesCS1D01G010700 chr6B 93.367 603 30 4 2092 2694 178505309 178505901 0.000000e+00 883.0
20 TraesCS1D01G010700 chr6B 88.506 174 10 2 7462 7635 257995328 257995491 1.360000e-47 202.0
21 TraesCS1D01G010700 chr6B 86.250 80 7 3 7631 7709 257995817 257995893 5.120000e-12 84.2
22 TraesCS1D01G010700 chr4D 93.613 595 30 2 2092 2686 154755610 154755024 0.000000e+00 881.0
23 TraesCS1D01G010700 chr6D 92.988 599 32 6 2092 2689 412532494 412533083 0.000000e+00 865.0
24 TraesCS1D01G010700 chr6D 94.872 78 4 0 7607 7684 147237701 147237624 1.090000e-23 122.0
25 TraesCS1D01G010700 chr5D 85.714 259 30 6 6474 6726 530925660 530925917 4.740000e-67 267.0
26 TraesCS1D01G010700 chr7B 94.872 78 4 0 3953 4030 566639071 566639148 1.090000e-23 122.0
27 TraesCS1D01G010700 chr5A 97.260 73 1 1 3958 4030 379130921 379130992 1.090000e-23 122.0
28 TraesCS1D01G010700 chr2B 94.872 78 3 1 3957 4033 417500764 417500841 3.910000e-23 121.0
29 TraesCS1D01G010700 chr4A 91.765 85 6 1 3953 4037 615196361 615196444 5.050000e-22 117.0
30 TraesCS1D01G010700 chr5B 82.524 103 14 4 6484 6583 670134451 670134552 3.960000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G010700 chr1D 5510403 5518371 7968 False 14717.0 14717 100.0000 1 7969 1 chr1D.!!$F1 7968
1 TraesCS1D01G010700 chr1A 7178189 7185518 7329 False 5246.0 7875 92.2945 856 7969 2 chr1A.!!$F2 7113
2 TraesCS1D01G010700 chr1A 6977022 6978198 1176 False 853.0 898 93.0040 856 2046 2 chr1A.!!$F1 1190
3 TraesCS1D01G010700 chr1B 8248561 8255780 7219 False 1985.2 2878 93.7990 856 7969 5 chr1B.!!$F1 7113
4 TraesCS1D01G010700 chr3D 555196711 555197297 586 False 909.0 909 94.4540 2092 2686 1 chr3D.!!$F1 594
5 TraesCS1D01G010700 chr3D 550607715 550608301 586 True 904.0 904 94.2860 2092 2686 1 chr3D.!!$R2 594
6 TraesCS1D01G010700 chr3D 555231624 555232210 586 True 876.0 876 93.4450 2092 2686 1 chr3D.!!$R3 594
7 TraesCS1D01G010700 chr7D 443545163 443545749 586 True 904.0 904 94.2860 2092 2686 1 chr7D.!!$R1 594
8 TraesCS1D01G010700 chr2D 385100535 385101121 586 False 893.0 893 93.9500 2092 2686 1 chr2D.!!$F1 594
9 TraesCS1D01G010700 chr6B 178505309 178505901 592 False 883.0 883 93.3670 2092 2694 1 chr6B.!!$F1 602
10 TraesCS1D01G010700 chr4D 154755024 154755610 586 True 881.0 881 93.6130 2092 2686 1 chr4D.!!$R1 594
11 TraesCS1D01G010700 chr6D 412532494 412533083 589 False 865.0 865 92.9880 2092 2689 1 chr6D.!!$F1 597


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
501 502 0.035056 CCCACCCACATGTCTTCTCC 60.035 60.000 0.00 0.00 0.00 3.71 F
502 503 0.035056 CCACCCACATGTCTTCTCCC 60.035 60.000 0.00 0.00 0.00 4.30 F
538 539 0.187361 CCGATCTCCTCTCCCCTCTT 59.813 60.000 0.00 0.00 0.00 2.85 F
549 550 0.264657 TCCCCTCTTGATCGATCCCA 59.735 55.000 22.31 8.46 0.00 4.37 F
550 551 0.394565 CCCCTCTTGATCGATCCCAC 59.605 60.000 22.31 0.00 0.00 4.61 F
1620 1969 0.810031 AGCGCACGGACATATTCACC 60.810 55.000 11.47 0.00 0.00 4.02 F
3317 3669 1.220206 CTCCTCGATGCTTGGCTGT 59.780 57.895 0.00 0.00 0.00 4.40 F
3433 3785 1.628846 ACTTGCCGTTTCTAGATGGGT 59.371 47.619 0.00 0.00 0.00 4.51 F
4453 4818 1.004628 TGGGTATGTGCTTCATGCTGT 59.995 47.619 9.34 0.00 43.37 4.40 F
4691 5056 0.675837 TGAGCTTGTCAGAGCATGGC 60.676 55.000 0.00 0.00 45.12 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 2025 0.038599 ATTGTCCACCAGCAGCATCA 59.961 50.000 0.00 0.00 0.00 3.07 R
2395 2746 0.541392 AGATAACTCATGGTGGCGCA 59.459 50.000 10.83 0.00 0.00 6.09 R
2518 2869 2.039746 TGGTACAGTAACAGCTGGCAAT 59.960 45.455 19.93 0.74 40.59 3.56 R
2735 3086 5.636121 CACTGCAGATACTTTACGGTAACAA 59.364 40.000 23.35 0.00 0.00 2.83 R
3057 3408 5.573219 AGGATCTGTGAAATGAACAATGGA 58.427 37.500 0.00 0.00 0.00 3.41 R
3477 3829 0.249031 GATGCAAGCCCCAATAACGC 60.249 55.000 0.00 0.00 0.00 4.84 R
4286 4651 1.719529 TTAGGACGGTCCTTCCACAA 58.280 50.000 32.91 18.62 46.91 3.33 R
4677 5042 2.032376 TGCGCCATGCTCTGACAA 59.968 55.556 4.18 0.00 46.63 3.18 R
6666 7275 0.473694 TGCCTTGACCTCTCCTCCAA 60.474 55.000 0.00 0.00 0.00 3.53 R
7150 7767 0.514255 CACATGGCAGACTGTTGACG 59.486 55.000 3.99 0.00 0.00 4.35 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)



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AutoCloner maintained by Alex Coulton.